Best way to "sculpt" sphere-shaped holes on a sphere surface?
If you use booleans and want smooth spheres as results, increase your original sphere segment counts, later on you can always retopologize if the resulting face count is too high. Starting from a highpoly mesh and working to a lower one can give acceptable results.

The implementation of Blender Booleans is from the Carve Library, this is what the blender dev has to say about how to use booleans (in another very similar question) -- link



The carve library has made it possible to do really nice booleans in blender, but you need sufficient geometry for the polygon based approach to retain smooth shapes.

Cleaner topology results come from being precise about matching up the level of sudivision where the objects interface each other. Taking a highly divided sphere like above and doing a difference with a scaled down sphere with identical vert count will produce more geometry than needed.

Ideally you will have similar face sizes like here:



Use the EdgeSplit Modifier, on smooth shaded faces, in combination with matching face sizes it looks acceptable.